Inflammatory Bowel Diseases (IBDs), namely ulcerative colitis (DC) and Crohn's disease (CD), are chronic, lifelong, relapsing illnesses, affecting close to 1 million Americans. Despite the many clues that a dysbiosis may exist in IBD, the specific changes in the microflora of IBD patients are largely unknown. Amplicon length heterogeneity (ALH) is a sophisticated and well established PCR based technology that can be used as a screening tool to identify changes in the Bacterial microflora of IBD patients. We therefore have hypothesized that the ileocolonic microflora in IBD has an altered microbial composition compared to normal microflora. We have gathered preliminary data that shows statistical differences between controls and IBD as well as within IBD patients. Therefore, to test the above hypothesis, we are proposing the following 2 inter-related scientific aims: AIM 1. Identify bacterial fingerprint patterns associated with IBD using ALH. ALH patterns will be determined in a total of 160 IBD patients and health controls and will be analyzed using diversity indeces, multivariate reduction analysis and cluster analysis. ALH patterns associated with IBD will be determined using histograms, ecological software in conjunction with custom PERL scripts as well as supervised and unsupervised automated pattern recognition systems. AIM 2.Determine the bacterial contents of putatively IBD associated ALH fingerprint patterns using molecular cloning and sequencing. Cloning and sequencing of targeted samples will be linked to bacterial identities by employing multiple bioinformatics tools. Significance. This proposal involves the first time use of a sophisticated and highly reproducible molecular biology tool, ALH, in the study of microflora in the Gl tract. There is a growing recognition of the importance of microflora in health and disease, including IBD. Studies that characterized microflora in human using powerful techniques from environmental microbiology such as ALH can bring about significant advances in the understanding of Gl tract illnesses. ALH may enable a real-time survey of microfloral changes for the first time in medicine and may provide the first evidence linking IBD with specific microbial patterns. [unreadable] [unreadable] [unreadable]